[BioC] Error in .nextMethod(e1, e2) with updated R and bioC package on MAC OS

Anat Caspi caspian at sas.upenn.edu
Sun Mar 30 21:13:29 CEST 2008

Hi Martin,

Thanks for your response. 
I've repeated the package installation as you recommended, in a new run of R.
I checked that I do not have any bioC packages loaded by default:
] getOption("defaultPackages")
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"

I also checked to see that I'm running v. 2.6.2:

the following was the message at startup-
R version 2.6.2 (2008-02-08)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

and I also invoked sessionInfo()
] sessionInfo()
R version 2.6.2 (2008-02-08)


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.2

I then followed by:
]    source("http://bioconductor.org/biocLite.R")
]    update.packages(repos=biocinstallRepos(), ask=FALSE)
The output began with:
also installing the dependency 'limma'

trying URL
Content type 'application/x-gzip' length 1064773 bytes (1.0 Mb)
opened URL

All subsequent packages passed with no warnings or errors except:

Error: cannot remove prior installation of package 'limma'

which is strange because it had just installed 'limma' as the first dependency.

Not sure where to go from here.
Thanks so much for your response.

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